Showing : desEQ2 • reset
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unequal number of treatmets to control
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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2
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848
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Batch effects removal across mRNA seq studies addressing different biological question: Best approach?
DESeq2
21 months ago Kuldeep • 0
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2
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830
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
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2
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857
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DESeq2 lfcShrink drastic shrinkage
DESeq2
updated 7 months ago by • 0 • written 21 months ago by • 0
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1.2k
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
21 months ago island • 0
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4
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1.4k
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DESeq2 aborting after upgrade
DESeq2
21 months ago Aarti • 0
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2
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836
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Cross-species analysis using DESeq2 - size factor computation
dese DESeq2
21 months ago pl23 • 0
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3
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1.1k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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3
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1.3k
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 21 months ago by • 0
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2
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1.9k
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Regressing out covariates from expression matrix for PCA visualization - can I use coefficients calculated in DESeq2??
DESeq2
21 months ago tombate94 • 0
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1
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1.1k
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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0
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926
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
21 months ago Jawahar • 0
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2
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816
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Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
22 months ago • updated 21 months ago JING • 0
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1
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532
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DESEQ2 reduced model input into Pathfindr
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1
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751
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 22 months ago by 43k • written 22 months ago by • 0
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2
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1.0k
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Deleting a column from data frame and then running DESeq2
DESeq2
updated 22 months ago by 43k • written 22 months ago by ▴ 10
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2
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1.8k
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Plotting mean TPM of an expressed gene
DESeq2
22 months ago • updated 21 months ago mp52226 • 0
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1
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859
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1
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598
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[DESEQ2] When to average biological replicates for hierarchical clustering
DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
2
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2
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615
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How to interpret log2fold values when using numeric contrasts in DESEQ2?
DESeq2
22 months ago pl23 • 0
1
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1
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666
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Looking for a MSigDB chip file
DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
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1
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1.0k
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DESeq2 multi-factor design and interaction terms
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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9
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2.4k
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
22 months ago Luca • 0
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1
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795
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
22 months ago WS • 0
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3
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2.7k
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DESeq2 design with multiple factors
DESeq2
written 22 months ago by • 0
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1
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1.0k
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 22 months ago by 43k • written 22 months ago by • 0
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3
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1.2k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 22 months ago by • 0
2
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2
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3.6k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
22 months ago Linton • 0
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5
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1.9k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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1
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986
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DESeq2 interaction term + sva
sva DESeq2
updated 22 months ago by 43k • written 23 months ago by ▴ 20
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3
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1.1k
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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1
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955
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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3
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3.6k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 22 months ago by ★ 1.4k • written 23 months ago by • 0
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6
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1.4k
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Deseq2 Coefficients from resultsNames() not reflecting all coefficient possibilities.
DESeq2
22 months ago • updated 21 months ago JalapenoCornbread • 0
2
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3
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1.4k
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lfcSE always positive. Does this make sense?
DESeq2
updated 22 months ago by 21k • written 22 months ago by • 0
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3
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862
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DESeq2: Difference in DEG numbers when switching reference condition (numerator, denominator) using contrast
DESeq2
updated 22 months ago by 43k • written 23 months ago by • 0
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2
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1.7k
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DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
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3
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1.1k
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DESeq2: the model matrix is not full rank issue
DESeq2
updated 22 months ago by • 0 • written 23 months ago by • 0
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3
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2.2k
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Difference between vst() and varianceStabilizingTransform()
DESeq2
written 23 months ago by • 0
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5
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1.2k
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Unexpected results for a differential expression analysis between males and females
DESeq2
updated 23 months ago by ★ 3.4k • written 23 months ago by • 0
0
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5
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2.3k
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scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
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4
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1.2k
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 22 months ago by 53k • written 23 months ago by • 0
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2
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809
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Running DESeq on normalized data
deseq DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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2
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1.2k
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Linear Model Fitting and Colinearity
dese DESeq2
23 months ago Hugo • 0
2
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1
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626
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removeBatchEffect with non-linear model fit
limma DESeq2
updated 23 months ago by 53k • written 23 months ago by • 0
1
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13
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2.4k
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 22 months ago by ★ 4.0k • written 23 months ago by ▴ 10
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1
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1.7k
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
1
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2
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859
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 10 weeks ago by ▴ 10 • written 23 months ago by • 0
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2
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2.4k
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DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
2
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2
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1.8k
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How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 23 months ago by • 0
4,836 results • Page 8 of 97
Recent ...
Replies
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
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